The most obvious reason is because Torchwood hadn't been invented yet but that's not good enough for fans who want this to a be a complete universe that doesn't contradict itself and wonder also why Pertwee era spin-offs sometimes do but also sometimes don't try and cover over the cracks.

Here's the fictional fantasy reason.

Torchwood hadn't been invented yet.

You might argue on this if you like, but time in the Doctor Who universe has always been in flux even within the fictional world of the series. So when the Doctor delays the Daleks for a thousand years in Genesis of the Daleks it does have a real effect in ensuing episodes and effectively overrides what may or may not have happened before in previous pepperpot related stories. Retconned if you will.

Similarly in nuWho, when Van Statten doesn't know what a Dalek is despite Journey's End, it's because that episode happened in the timeline before Journey's End changed everything. In the new timeline, there may or may not be a version of Dalek which reflects those events and Van Statten identifies the Dalek immediately. Assuming his collection hasn't already been impounded by Torchwood.

So now, post Tooth & Claw, there will be a version of the Pertwee era in which Torchwood is a going concern. If there are any classic Who spin-0ffs which mention Torchwood, they're happening in the new version of the timeline rather than the old one. Not that there needs to be much of a difference, probably, though there is some potential in producing a series of nuTrek style remakes which recreate old stories like The Claws of Axos or Invasion of the Dinosaurs in a nuWho tainted version of the timeline in which Torchwood does exist. The Delgado Master becomes a Scientific Advisor to the evil version of Torchwood.

In other words, time can be rewritten and many of the stories we've enjoyed across the years are just snapshots of a fictional universe at a certain moment.

Some notes:

(1) The Doctor can only change time if he wasn't previously aware of the outcome. In other words, he can't kill Hitler, even if he wanted to. The whole fixed point in time business. Notice that whenever he's tried, the aforementioned Genesis, Waters of Mars, something has always happened to keep the web of time in check, even if that includes, as per Father's Day, the destruction of a planet or timeline.

(2) All of which also in effect nullifies canonicity questions because it means that everything can happen, even Death Comes To Time. They're just different versions of the fictional truth. At some point, there's nothing to say that there isn't a version of the timeline in which the Doctor isn't a eccentric human in 60s London, the TARDIS his personal hobby. Chameleon arch or whatever.